Fig 1.
Workflow for library preparation and sequencing.
Amplicons generated through a PGMY PCR were amplified using customized primers containing Miseq specific adaptors then indexation and pooling were done before sequencing using Miseq plateform.
Fig 2.
The designed pipeline for HPV genotyping in this study contains 3 steps: reads quality control to remove bad quality reads, processing of retained reads for mapping into Human genome, and finally in the final set of selected sequences the viruses were detected and genotyped by assembly and contigs mapping to HPV reference genome.
Fig 3.
HPV-aligned reads vs. total number of reads according to HPV status and number of HPV types in the samples.
There was no difference in total reads number between positive samples (blue dots) and negative samples (red dots). In contrast, alignment of HPV reads depended on the HPV types in each positive sample (p<10−3): The aligned HPV reads were more numerous in samples having multiple infections (HPV types number >1): the size of dots indicates the number of HPV types in each types sample.
Table 1.
Proficiency test panel genotyping using NGS technology.
Fig 4.
Detected HPV types by NGS and comparison with RLH.
Table 2.
Summary of the comparison between NGS and RLH genotyping assays.